Contacts of the strand formed by residues 195 - 200 (chain B) in PDB entry 3QI2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 195 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL* 3.2 26.4 + - - +
189B PHE 4.0 3.4 - - - -
190B THR* 3.4 26.1 + - + +
193B ASP 5.0 5.5 + - - -
194B LEU* 1.3 73.0 - - - +
196B PHE* 1.3 63.4 + - - +
197B LYS* 3.9 8.5 + - + +
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Residues in contact with PHE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL* 3.4 26.0 - - + -
36B LEU* 3.7 27.4 - - + -
187B THR 4.6 0.4 - - - -
188B HIS* 3.6 5.7 + - - +
189B PHE* 2.9 64.6 + + + +
191B PHE* 3.6 20.4 - + + -
194B LEU* 3.3 42.8 - - + -
195B HIS* 1.3 73.4 - - - +
197B LYS* 1.3 64.4 + - - +
198B MET 4.0 1.3 - - - +
336B PHE* 3.8 14.1 - + - -
340B THR* 4.0 19.7 - - + -
343B ILE* 4.4 10.8 - - + -
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Residues in contact with LYS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL 3.4 17.6 + - - +
35B LYS* 4.0 3.2 - - + +
36B LEU* 3.6 14.7 + - - +
186B GLU* 5.5 0.2 - - - -
187B THR 3.8 5.6 - - - -
188B HIS* 3.1 33.1 - - + +
195B HIS* 4.6 8.5 - - - +
196B PHE* 1.3 76.6 - - - +
198B MET* 1.3 58.6 + - - +
199B PHE* 3.0 36.3 + - + -
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Residues in contact with MET 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.5 36.3 - - + +
38B LEU* 3.8 33.9 - - + -
49B ILE* 4.1 11.2 - - + -
50B VAL* 3.9 14.6 - - + +
53B MET* 3.6 41.7 - - + -
186B GLU* 3.1 25.6 - - - +
187B THR* 3.2 21.8 + - + +
189B PHE* 4.5 7.0 - - + -
196B PHE* 4.0 1.0 - - - +
197B LYS* 1.3 72.3 - - - +
199B PHE* 1.3 61.6 + - - +
200B ASP 4.1 0.2 + - - -
222B ILE* 4.5 9.2 - - + -
336B PHE* 4.1 4.0 - - + -
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Residues in contact with PHE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS* 4.2 29.2 - - + -
36B LEU 2.9 11.4 + - - +
37B LEU* 3.4 18.7 - - + +
38B LEU* 2.9 27.2 + - - -
184B ILE* 5.5 7.0 - - + -
185B VAL 3.5 3.6 - - - -
186B GLU* 3.3 36.8 - - + -
188B HIS* 4.8 2.9 - + - -
197B LYS* 3.0 53.2 - - + -
198B MET* 1.3 74.5 - - - +
200B ASP* 1.3 60.9 + - - +
201B VAL 4.2 0.2 - - - -
214B CYS* 5.1 7.9 - - + -
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Residues in contact with ASP 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU* 3.9 19.8 - - + +
46B LYS* 3.5 33.1 - - - +
47B SER* 3.6 27.5 + - - -
50B VAL* 3.9 11.0 - - + -
181B THR* 5.7 0.2 + - - -
185B VAL* 2.8 41.7 + - + +
198B MET 4.1 1.4 + - - -
199B PHE* 1.3 72.1 - - - +
201B VAL* 1.3 76.9 + - - +
202B GLY* 3.5 12.4 + - - -
356B GDP 4.4 1.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il